Results for the regional assessment (PhD Chapter 1)

Workspace preparation
Maps
- 1. General map
- 2. Parameters maps
Analyses

This series of files compile all analyses done during Chapter 1 for the regional assessment (Campaign 2016).

Section 1 regroups maps, graphical ordinations and clustering.
Section 2 presents SIMPER and regressions results.

All analyses have been done with PRIMER-e 6 and R 3.6.0.

Caracteristics of each campaign

		2014	2016	2017
Sampling date		August-September	June to August	July
Criteria for perturbation		Potentially impacted if close to the city or industries, References outside the bay	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered		BSI	BSI, CPC, BDA, MR	BSI, MR
Number of sampled stations		40 (20 HI, 20 R)	78 (26 BSI, 19 CPC, 18 BDA, 15 MR)	126 (111 BSI, 15 MR)
Parameters sampled	Organic matter	yes	yes	yes
	Photosynthetic pigments	no	yes	yes
	Sediment grain-size	yes	yes	yes
	Heavy-metals	yes	yes (for a limited number of stations)	no (interpolated based on 2014 and 2016 values)
Benthic communities	Compartment targeted	Macro-infauna	Macro-infauna	Macro-infauna
	Sieved used	500 µm	1 mm	500 µm and 1 mm
	Conservation technique	Formaldehyle	Formaldehyle	Formaldehyle
Others		N.A.	N.A.	N.A.

Click on the table of contents in the left margin to assess a specific analysis
Click on a figure to zoom it

To assess Section 2, click here.
To go back to the summary page, click here.

We selected variables and characteristic species (using IndVal index and SIMPER procedure, see Section 2) for the analyses:

Depth of the station: depth
Percentage of organic matter: om
Percentage of gravel: gravel
Percentage of sand: sand
Percentage of silt: silt
Percentage of clay: clay
Concentration of arsenic: arsenic
Concentration of cadmium: cadmium
Concentration of chromium: chromium
Concentration of copper: copper
Concentration of iron: iron
Concentration of manganese: manganese
Concentration of mercury: mercury
Concentration of lead: lead
Concentration of zinc: zinc
Species richness: S
Abundance of total individuals: N
Shannon index: H
Piélou evenness: J
Abundance of Mesodesma arctatum: Marc
Abundance of Cistenides granulata: Cgra

As there is missing data for metal concentrations outside BSI, two Designs have been used:

Design 1: stations at BSI, CPC, BDA, MR with only habitat parameters
Design 2: stations at BSI with habitat parameters and heavy metal concentrations.

Workspace preparation

setwd("Documents/PROJECTS/Chap1")

# library(clustsig)
library(dendextend)
library(FactoMineR)
library(graphicsutils)
library(pander)
library(plotrix)
library(RColorBrewer)
library(reshape2)
library(sf)
library(stats)
library(tidyverse)
library(vegan)

source("Chap1_data_import.R")

Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.

Maps

1. General map

2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity.

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Cgra

Marc

Epar

Species richness

Total abundance

Shannon index

Piélou’s evenness

Analyses

1. Barplots

Depth

Organic matter

Grain-size

Heavy metals

This section is not relevant here, as we only have data for BSI.

Species abundances

Diversity indices

2. Phylum frequencies

Phylum abundances by region
Phylum	BSI	CPC	BDA	MR
Annelida	214	69	188	43
Mollusca	191	45	89	100
Arthropoda	119	13	30	43
Echinodermata	27	206	24	138
Platyhelminthes	3	0	0	0
Nematoda	2	0	0	0
Nemertea	1	0	0	0
Brachiopoda	0	0	0	2
Cnidaria	0	0	0	1
Hemichordata	0	0	0	0
Phoronida	0	0	0	0
Sipuncula	0	0	0	0